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- PDB-1l1o: Structure of the human Replication Protein A (RPA) trimerization core -

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Basic information

Entry
Database: PDB / ID: 1l1o
TitleStructure of the human Replication Protein A (RPA) trimerization core
Components
  • Replication protein A 14 kDa subunit
  • Replication protein A 32 kDa subunit
  • Replication protein A 70 kDa DNA-binding subunit
KeywordsDNA BINDING PROTEIN / eukaryotic SSB / ssDNA binding protein / OB-fold
Function / homology
Function and homology information


protein localization to chromosome / DNA replication factor A complex / lateral element / regulation of DNA damage checkpoint / single-stranded telomeric DNA binding / G-rich strand telomeric DNA binding / Removal of the Flap Intermediate / chromatin-protein adaptor activity / protein localization to site of double-strand break / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) ...protein localization to chromosome / DNA replication factor A complex / lateral element / regulation of DNA damage checkpoint / single-stranded telomeric DNA binding / G-rich strand telomeric DNA binding / Removal of the Flap Intermediate / chromatin-protein adaptor activity / protein localization to site of double-strand break / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Removal of the Flap Intermediate from the C-strand / HDR through Single Strand Annealing (SSA) / regulation of double-strand break repair via homologous recombination / telomeric DNA binding / Impaired BRCA2 binding to RAD51 / hemopoiesis / Presynaptic phase of homologous DNA pairing and strand exchange / site of DNA damage / PCNA-Dependent Long Patch Base Excision Repair / Regulation of HSF1-mediated heat shock response / Activation of the pre-replicative complex / HSF1 activation / telomere maintenance via telomerase / mismatch repair / Activation of ATR in response to replication stress / SUMOylation of DNA damage response and repair proteins / mitotic G1 DNA damage checkpoint signaling / homeostasis of number of cells within a tissue / telomere maintenance / regulation of mitotic cell cycle / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / meiotic cell cycle / male germ cell nucleus / nucleotide-excision repair / Fanconi Anemia Pathway / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / double-strand break repair via homologous recombination / base-excision repair / PML body / G2/M DNA damage checkpoint / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / Meiotic recombination / DNA-templated DNA replication / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / single-stranded DNA binding / regulation of cell population proliferation / site of double-strand break / Processing of DNA double-strand break ends / protein phosphatase binding / DNA recombination / Regulation of TP53 Activity through Phosphorylation / in utero embryonic development / damaged DNA binding / chromosome, telomeric region / DNA replication / nuclear body / DNA repair / positive regulation of cell population proliferation / DNA damage response / ubiquitin protein ligase binding / chromatin binding / chromatin / enzyme binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Replication factor A protein 2 / Replication protein A, C-terminal / Replication protein A C terminal / Replication factor A protein 3 / Replication factor A protein 3 / Replication factor-A protein 1, N-terminal domain / Replication factor A protein-like / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain ...Replication factor A protein 2 / Replication protein A, C-terminal / Replication protein A C terminal / Replication factor A protein 3 / Replication factor A protein 3 / Replication factor-A protein 1, N-terminal domain / Replication factor A protein-like / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / : / Replication factor A, C-terminal / Replication factor-A C terminal domain / N-terminal domain of TfIIb - #10 / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / N-terminal domain of TfIIb / Single Sheet / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Replication protein A 32 kDa subunit / Replication protein A 70 kDa DNA-binding subunit / Replication protein A 14 kDa subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsBochkareva, E.V. / Korolev, S. / Lees-Miller, S.P. / Bochkarev, A.
Citation
Journal: EMBO J. / Year: 2002
Title: Structure of the RPA trimerization core and its role in the multistep DNA-binding mechanism of RPA.
Authors: Bochkareva, E. / Korolev, S. / Lees-Miller, S.P. / Bochkarev, A.
#1: Journal: J.Biol.Chem. / Year: 2000
Title: The role for zinc in replication protein A.
Authors: Bochkareva, E. / Korolev, S. / Bochkarev, A.
History
DepositionFeb 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX AUTHOR PROVIDED SECONDARY STRUCTURE.
Remark 700SHEET AUTHOR PROVIDED SHEET RECORDS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Replication protein A 14 kDa subunit
B: Replication protein A 32 kDa subunit
C: Replication protein A 70 kDa DNA-binding subunit
D: Replication protein A 14 kDa subunit
E: Replication protein A 32 kDa subunit
F: Replication protein A 70 kDa DNA-binding subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,3138
Polymers98,1826
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.527, 88.527, 341.090
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsRPA is a heterotrimer made of RPA70, RPA32, and RPA14 subunits

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Components

#1: Protein Replication protein A 14 kDa subunit


Mass: 13583.714 Da / Num. of mol.: 2 / Fragment: RPA14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RFA3_HUMAN / Plasmid: pET15B 3-core / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P35244
#2: Protein Replication protein A 32 kDa subunit


Mass: 14361.513 Da / Num. of mol.: 2 / Fragment: RPA32 central domain (residues 44-171)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RFA2_HUMAN / Plasmid: pET15B 3-core / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P15927
#3: Protein Replication protein A 70 kDa DNA-binding subunit


Mass: 21145.850 Da / Num. of mol.: 2 / Fragment: RPA70 C-terminal domain (residues 436-616)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RFA1_HUMAN / Plasmid: pET15B 3-core / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P27694
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.93 Å3/Da / Density % sol: 68.69 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.1 M Hepes, 9% glycerol, and 1.6 M ammonium sulfate, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 300K
Crystal grow
*PLUS
Details: Bochkareva, E., (2000) J.Biol.Chem., 275, 27332.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 MHEPES1reservoirpH7.8
29 %glycerol1reservoir
31.6 Mammonium sulfate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONAPS 19-ID11.0081.008
SYNCHROTRONAPS 19-ID20.9790.979
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDSep 5, 1999
ADSC QUANTUM 42CCDSep 5, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0081
20.9791
ReflectionResolution: 2.7→20 Å / Num. obs: 43573 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 68.5 Å2 / Rsym value: 0.062 / Net I/σ(I): 2.7
Reflection shellResolution: 2.7→2.8 Å / Mean I/σ(I) obs: 2.7 / Num. unique all: 4302 / Rsym value: 0.532 / % possible all: 99.7
Reflection
*PLUS
Num. measured all: 233991 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 99.7 % / Rmerge(I) obs: 0.532

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Processing

Software
NameVersionClassification
SHARPphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.8→19.92 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 584448.25 / Data cutoff high rms absF: 584448.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 3681 10.2 %RANDOM
Rwork0.236 ---
all0.245 38232 --
obs0.236 36244 92.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.918 Å2 / ksol: 0.323875 e/Å3
Displacement parametersBiso mean: 59.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å27.77 Å20 Å2
2--0.86 Å20 Å2
3----1.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6569 0 2 0 6571
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_improper_angle_d1.41
X-RAY DIFFRACTIONc_mcbond_it2.712.5
X-RAY DIFFRACTIONc_mcangle_it4.53
X-RAY DIFFRACTIONc_scbond_it3.213
X-RAY DIFFRACTIONc_scangle_it4.813.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.373 511 10.5 %
Rwork0.336 4374 -
obs--75.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3&_1_PARAMETER_INFILE_3&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4&_1_PARAMETER_INFILE_4&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5
Refinement
*PLUS
% reflection Rfree: 9.4 % / Rfactor all: 0.245 / Rfactor obs: 0.236 / Rfactor Rfree: 0.283 / Rfactor Rwork: 0.236
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.41
LS refinement shell
*PLUS
Rfactor Rfree: 0.373 / Rfactor Rwork: 0.336 / Rfactor obs: 0.336

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